1
|
Pathak S, Strader LC. GRP7 phase separation as an interpreter of temperature cues. MOLECULAR PLANT 2024; 17:842-844. [PMID: 38664969 DOI: 10.1016/j.molp.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/20/2024] [Accepted: 04/21/2024] [Indexed: 05/31/2024]
Affiliation(s)
- Sunita Pathak
- Department of Biology, Duke University, Durham, NC, USA
| | | |
Collapse
|
2
|
Khassanova G, Oshergina I, Ten E, Jatayev S, Zhanbyrshina N, Gabdola A, Gupta NK, Schramm C, Pupulin A, Philp-Dutton L, Anderson P, Sweetman C, Jenkins CL, Soole KL, Shavrukov Y. Zinc finger knuckle genes are associated with tolerance to drought and dehydration in chickpea ( Cicer arietinum L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1354413. [PMID: 38766473 PMCID: PMC11099236 DOI: 10.3389/fpls.2024.1354413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/17/2024] [Indexed: 05/22/2024]
Abstract
Chickpea (Cicer arietinum L.) is a very important food legume and needs improved drought tolerance for higher seed production in dry environments. The aim of this study was to determine diversity and genetic polymorphism in zinc finger knuckle genes with CCHC domains and their functional analysis for practical improvement of chickpea breeding. Two CaZF-CCHC genes, Ca04468 and Ca07571, were identified as potentially important candidates associated with plant responses to drought and dehydration. To study these genes, various methods were used including Sanger sequencing, DArT (Diversity array technology) and molecular markers for plant genotyping, gene expression analysis using RT-qPCR, and associations with seed-related traits in chickpea plants grown in field trials. These genes were studied for genetic polymorphism among a set of chickpea accessions, and one SNP was selected for further study from four identified SNPs between the promoter regions of each of the two genes. Molecular markers were developed for the SNP and verified using the ASQ and CAPS methods. Genotyping of parents and selected breeding lines from two hybrid populations, and SNP positions on chromosomes with haplotype identification, were confirmed using DArT microarray analysis. Differential expression profiles were identified in the parents and the hybrid populations under gradual drought and rapid dehydration. The SNP-based genotypes were differentially associated with seed weight per plant but not with 100 seed weight. The two developed and verified SNP molecular markers for both genes, Ca04468 and Ca07571, respectively, could be used for marker-assisted selection in novel chickpea cultivars with improved tolerance to drought and dehydration.
Collapse
Affiliation(s)
- Gulmira Khassanova
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
- Department of Crop Breeding, A.I.Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Irina Oshergina
- Department of Crop Breeding, A.I.Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Evgeniy Ten
- Department of Crop Breeding, A.I.Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
| | - Nursaule Zhanbyrshina
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
| | - Ademi Gabdola
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
| | - Narendra K. Gupta
- Department of Plant Physiology, Sri Karan Narendra (SNK) Agricultural University, Jobster, Rajastan, India
| | - Carly Schramm
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Antonio Pupulin
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Lauren Philp-Dutton
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Peter Anderson
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Crystal Sweetman
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Colin L.D. Jenkins
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Kathleen L. Soole
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Yuri Shavrukov
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| |
Collapse
|
3
|
Xu F, Wang L, Li Y, Shi J, Staiger D, Yu F. Phase separation of GRP7 facilitated by FERONIA-mediated phosphorylation inhibits mRNA translation to modulate plant temperature resilience. MOLECULAR PLANT 2024; 17:460-477. [PMID: 38327052 DOI: 10.1016/j.molp.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 01/07/2024] [Accepted: 02/01/2024] [Indexed: 02/09/2024]
Abstract
Changes in ambient temperature profoundly affect plant growth and performance. Therefore, the molecular basis of plant acclimation to temperature fluctuation is of great interest. In this study, we discovered that GLYCINE-RICH RNA-BINDING PROTEIN 7 (GRP7) contributes to cold and heat tolerance in Arabidopsis thaliana. We found that exposure to a warm temperature rapidly induces GRP7 condensates in planta, which can be reversed by transfer to a lower temperature. Cell biology and biochemical assays revealed that GRP7 undergoes liquid-liquid phase separation (LLPS) in vivo and in vitro. LLPS of GRP7 in the cytoplasm contributes to the formation of stress granules that recruit RNA, along with the translation machinery component eukaryotic initiation factor 4E1 (eIF4E1) and the mRNA chaperones COLD SHOCK PROTEIN 1 (CSP1) and CSP3, to inhibit translation. Moreover, natural variations in GRP7 affecting the residue phosphorylated by the receptor kinase FERONIA alter its capacity to undergo LLPS and correlate with the adaptation of some Arabidopsis accessions to a wider temperature range. Taken together, our findings illustrate the role of translational control mediated by GRP7 LLPS to confer plants with temperature resilience.
Collapse
Affiliation(s)
- Fan Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Long Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China; State Key Laboratory of Hybrid Rice, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, P.R. China
| | - Yingbin Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Junfeng Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China.
| |
Collapse
|
4
|
Li J, Zhao R, Liu J, Yao J, Ma S, Yin K, Zhang Y, Liu Z, Yan C, Zhao N, Zhou X, Chen S. Populus euphratica GRP2 Interacts with Target mRNAs to Negatively Regulate Salt Tolerance by Interfering with Photosynthesis, Na +, and ROS Homeostasis. Int J Mol Sci 2024; 25:2046. [PMID: 38396725 PMCID: PMC10888501 DOI: 10.3390/ijms25042046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/17/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
The transcription of glycine-rich RNA-binding protein 2 (PeGRP2) transiently increased in the roots and shoots of Populus euphratica (a salt-resistant poplar) upon initial salt exposure and tended to decrease after long-term NaCl stress (100 mM, 12 days). PeGRP2 overexpression in the hybrid Populus tremula × P. alba '717-1B4' (P. × canescens) increased its salt sensitivity, which was reflected in the plant's growth and photosynthesis. PeGRP2 contains a conserved RNA recognition motif domain at the N-terminus, and RNA affinity purification (RAP) sequencing was developed to enrich the target mRNAs that physically interacted with PeGRP2 in P. × canescens. RAP sequencing combined with RT-qPCR revealed that NaCl decreased the transcripts of PeGRP2-interacting mRNAs encoding photosynthetic proteins, antioxidative enzymes, ATPases, and Na+/H+ antiporters in this transgenic poplar. Specifically, PeGRP2 negatively affected the stability of the target mRNAs encoding the photosynthetic proteins PETC and RBCMT; antioxidant enzymes SOD[Mn], CDSP32, and CYB1-2; ATPases AHA11, ACA8, and ACA9; and the Na+/H+ antiporter NHA1. This resulted in (i) a greater reduction in Fv/Fm, YII, ETR, and Pn; (ii) less pronounced activation of antioxidative enzymes; and (iii) a reduced ability to maintain Na+ homeostasis in the transgenic poplars during long-term salt stress, leading to their lowered ability to tolerate salinity stress.
Collapse
Affiliation(s)
- Jing Li
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Rui Zhao
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Jian Liu
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Jun Yao
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China;
| | - Siyuan Ma
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Kexin Yin
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Ying Zhang
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Zhe Liu
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Caixia Yan
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Nan Zhao
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Xiaoyang Zhou
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Shaoliang Chen
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| |
Collapse
|
5
|
Dishliyska V, Stoyancheva G, Abrashev R, Miteva-Staleva J, Spasova B, Angelova M, Krumova E. Catalase from the Antarctic Fungus Aspergillus fumigatus I-9-Biosynthesis and Gene Characterization. Indian J Microbiol 2023; 63:541-548. [PMID: 38031622 PMCID: PMC10682308 DOI: 10.1007/s12088-023-01110-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/07/2023] [Indexed: 12/01/2023] Open
Abstract
Extremely cold habitats are a serious challenge for the existing there organisms. Inhabitants of these conditions are mostly microorganisms and lower mycetae. The mechanisms of microbial adaptation to extreme conditions are still unclear. Low temperatures cause significant physiological and biochemical changes in cells. Recently, there has been increasing interest in the relationship between low-temperature exposure and oxidative stress events, as well as the importance of antioxidant enzymes for survival in such conditions. The catalase is involved in the first line of the cells' antioxidant defense. Published information supports the concept of a key role for catalase in antioxidant defense against cold stress in a wide range of organisms isolated from the Antarctic. Data on representatives of microscopic fungi, however, are rarely found. There is scarce information on the characterization of catalase synthesized by adapted to cold stress organisms. Overall, this study aimed to observe the role of catalase in the survival strategy of filamentous fungi in extremely cold habitats and to identify the gene encoded catalase enzyme. Our results clearly showed that catalase is the main part of antioxidant enzyme defense in fungal cells against oxidative stress caused by low temperature exposure.
Collapse
Affiliation(s)
- Vladislava Dishliyska
- Departament of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G, Bonchev Str. Bl.26, 1113 Sofia, Bulgaria
| | - Galina Stoyancheva
- Departament of General Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G, Bonchev Str. Bl.26, 1113 Sofia, Bulgaria
| | - Radoslav Abrashev
- Departament of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G, Bonchev Str. Bl.26, 1113 Sofia, Bulgaria
| | - Jeny Miteva-Staleva
- Departament of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G, Bonchev Str. Bl.26, 1113 Sofia, Bulgaria
| | - Boriana Spasova
- Departament of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G, Bonchev Str. Bl.26, 1113 Sofia, Bulgaria
| | - Maria Angelova
- Departament of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G, Bonchev Str. Bl.26, 1113 Sofia, Bulgaria
| | - Ekaterina Krumova
- Departament of Mycology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G, Bonchev Str. Bl.26, 1113 Sofia, Bulgaria
| |
Collapse
|
6
|
Mateos JL, Staiger D. Toward a systems view on RNA-binding proteins and associated RNAs in plants: Guilt by association. THE PLANT CELL 2023; 35:1708-1726. [PMID: 36461946 PMCID: PMC10226577 DOI: 10.1093/plcell/koac345] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/08/2022] [Accepted: 11/17/2022] [Indexed: 05/30/2023]
Abstract
RNA-binding proteins (RBPs) have a broad impact on most biochemical, physiological, and developmental processes in a plant's life. RBPs engage in an on-off relationship with their RNA partners, accompanying virtually every stage in RNA processing and function. While the function of a plethora of RBPs in plant development and stress responses has been described, we are lacking a systems-level understanding of components in RNA-based regulation. Novel techniques have substantially enlarged the compendium of proteins with experimental evidence for binding to RNAs in the cell, the RNA-binding proteome. Furthermore, ribonomics methods have been adapted for use in plants to profile the in vivo binding repertoire of RBPs genome-wide. Here, we discuss how recent technological achievements have provided novel insights into the mode of action of plant RBPs at a genome-wide scale. Furthermore, we touch upon two emerging topics, the connection of RBPs to phase separation in the cell and to extracellular RNAs. Finally, we define open questions to be addressed to move toward an integrated understanding of RBP function.
Collapse
Affiliation(s)
- Julieta L Mateos
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET-UBA), Buenos Aires, Argentina
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| |
Collapse
|
7
|
Yan Y, Gan J, Tao Y, Okita TW, Tian L. RNA-Binding Proteins: The Key Modulator in Stress Granule Formation and Abiotic Stress Response. FRONTIERS IN PLANT SCIENCE 2022; 13:882596. [PMID: 35783947 PMCID: PMC9240754 DOI: 10.3389/fpls.2022.882596] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/04/2022] [Indexed: 05/08/2023]
Abstract
To cope with abiotic environmental stress, plants rapidly change their gene expression transcriptionally and post-transcriptionally, the latter by translational suppression of selected proteins and the assembly of cytoplasmic stress granules (SGs) that sequester mRNA transcripts. RNA-binding proteins (RBPs) are the major players in these post-transcriptional processes, which control RNA processing in the nucleus, their export from the nucleus, and overall RNA metabolism in the cytoplasm. Because of their diverse modular domain structures, various RBP types dynamically co-assemble with their targeted RNAs and interacting proteins to form SGs, a process that finely regulates stress-responsive gene expression. This review summarizes recent findings on the involvement of RBPs in adapting plants to various abiotic stresses via modulation of specific gene expression events and SG formation. The relationship of these processes with the stress hormone abscisic acid (ABA) is discussed.
Collapse
Affiliation(s)
- Yanyan Yan
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable (Ministry of Agriculture and Rural Affairs), Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Jianghuang Gan
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable (Ministry of Agriculture and Rural Affairs), Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Yilin Tao
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable (Ministry of Agriculture and Rural Affairs), Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Thomas W. Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
- *Correspondence: Thomas W. Okita,
| | - Li Tian
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable (Ministry of Agriculture and Rural Affairs), Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
- Li Tian,
| |
Collapse
|
8
|
Shim JS, Park SH, Lee DK, Kim YS, Park SC, Redillas MCFR, Seo JS, Kim JK. The Rice GLYCINE-RICH PROTEIN 3 Confers Drought Tolerance by Regulating mRNA Stability of ROS Scavenging-Related Genes. RICE (NEW YORK, N.Y.) 2021; 14:31. [PMID: 33742286 PMCID: PMC7979854 DOI: 10.1186/s12284-021-00473-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/10/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Plant glycine-rich proteins are categorized into several classes based on their protein structures. The glycine-rich RNA binding proteins (GRPs) are members of class IV subfamily possessing N-terminus RNA-recognition motifs (RRMs) and proposed to be involved in post-transcriptional regulation of its target transcripts. GRPs are involved in developmental process and cellular stress responses, but the molecular mechanisms underlying these regulations are still elusive. RESULTS Here, we report the functional characterization of rice GLYCINE-RICH PROTEIN 3 (OsGRP3) and its physiological roles in drought stress response. Both drought stress and ABA induce the expression of OsGRP3. Transgenic plants overexpressing OsGRP3 (OsGRP3OE) exhibited tolerance while knock-down plants (OsGRP3KD) were susceptible to drought compared to the non-transgenic control. In vivo, subcellular localization analysis revealed that OsGRP3-GFP was transported from cytoplasm/nucleus into cytoplasmic foci following exposure to ABA and mannitol treatments. Comparative transcriptomic analysis between OsGRP3OE and OsGRP3KD plants suggests that OsGRP3 is involved in the regulation of the ROS related genes. RNA-immunoprecipitation analysis revealed the associations of OsGRP3 with PATHOGENESIS RELATED GENE 5 (PR5), METALLOTHIONEIN 1d (MT1d), 4,5-DOPA-DIOXYGENASE (DOPA), and LIPOXYGENASE (LOX) transcripts. The half-life analysis showed that PR5 transcripts decayed slower in OsGRP3OE but faster in OsGRP3KD, while MT1d and LOX transcripts decayed faster in OsGRP3OE but slower in OsGRP3KD plants. H2O2 accumulation was reduced in OsGRP3OE and increased in OsGRP3KD plants compared to non-transgenic plants (NT) under drought stress. CONCLUSION OsGRP3 plays a positive regulator in rice drought tolerance and modulates the transcript level and mRNA stability of stress-responsive genes, including ROS-related genes. Moreover, OsGRP3 contributes to the reduction of ROS accumulation during drought stress. Our results suggested that OsGRP3 alleviates ROS accumulation by regulating ROS-related genes' mRNA stability under drought stress, which confers drought tolerance.
Collapse
Affiliation(s)
- Jae Sung Shim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, South Korea
| | - Su-Hyun Park
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Dong-Keun Lee
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- E GREEN GLOBAL, Gunpo, 15843, South Korea
| | - Youn Shic Kim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon, 24341, South Korea
| | - Soo-Chul Park
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju, 54874, South Korea
| | | | - Jun Sung Seo
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea.
| | - Ju-Kon Kim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, South Korea.
| |
Collapse
|
9
|
Liu C, Schläppi MR, Mao B, Wang W, Wang A, Chu C. The bZIP73 transcription factor controls rice cold tolerance at the reproductive stage. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1834-1849. [PMID: 30811812 PMCID: PMC6686130 DOI: 10.1111/pbi.13104] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 02/19/2019] [Accepted: 02/23/2019] [Indexed: 05/19/2023]
Abstract
Cold temperature during the reproductive stage often causes great yield loss of grain crops in subtropical and temperate regions. Previously we showed that the rice transcription factor bZIP73Jap plays an important role in cold adaptation at the seedling stage. Here we further demonstrate that bZIP73Jap also confers cold stress tolerance at the reproductive stage. bZIP73Jap was up-regulated under cold treatment and predominately expressed in panicles at the early binucleate and flowering stages. bZIP73Jap forms heterodimers with bZIP71, and co-expression of bZIP73Jap and bZIP71 transgenic lines significantly increased seed-setting rate and grain yield under natural cold stress conditions. bZIP73Jap :bZIP71 not only repressed ABA level in anthers, but also enhanced soluble sugar transport from anthers to pollens and improved pollen grain fertility, seed-setting rate, and grain yield. Interestingly, bZIP73Jap :bZIP71 also regulated the expression of qLTG3-1Nip , and qLTG3-1Nip overexpression lines greatly improved rice tolerance to cold stress during the reproductive stage. Therefore, our work establishes a framework for rice cold stress tolerance through the bZIP71-bZIP73Jap -qLTG3-1Nip -sugar transport pathway. Together with our previous work, our results provide a powerful tool for improving rice cold stress tolerance at both the seedling and the reproductive stages.
Collapse
Affiliation(s)
- Citao Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | | | - Bigang Mao
- State Key Laboratory of Hybrid RiceChina National Hybrid Rice Research and Development CenterChangshaChina
| | - Wei Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Aiju Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| |
Collapse
|
10
|
Yeap WC, Namasivayam P, Ooi TEK, Appleton DR, Kulaveerasingam H, Ho CL. EgRBP42 from oil palm enhances adaptation to stress in Arabidopsis through regulation of nucleocytoplasmic transport of stress-responsive mRNAs. PLANT, CELL & ENVIRONMENT 2019; 42:1657-1673. [PMID: 30549047 DOI: 10.1111/pce.13503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 12/11/2018] [Indexed: 06/09/2023]
Abstract
Abiotic stress reduces plant growth and crop productivity. However, the mechanism underlying posttranscriptional regulations of stress response remains elusive. Herein, we report the posttranscriptional mechanism of nucleocytoplasmic RNA transport of stress-responsive transcripts mediated by EgRBP42, a heterogeneous nuclear ribonucleoprotein-like RNA-binding protein from oil palm, which could be necessary for rapid protein translation to confer abiotic stress tolerance in plants. Transgenic Arabidopsis overexpressing EgRBP42 showed early flowering through alteration of gene expression of flowering regulators and exhibited tolerance towards heat, cold, drought, flood, and salinity stresses with enhanced poststress recovery response by increasing the expression of its target stress-responsive genes. EgRBP42 harbours nucleocytoplasmic shuttling activity mediated by the nuclear localization signal and the M9-like domain of EgRBP42 and interacts directly with regulators in the nucleus, membrane, and the cytoplasm. EgRBP42 regulates the nucleocytoplasmic RNA transport of target stress-responsive transcripts through direct binding to their AG-rich motifs. Additionally, EgRBP42 transcript and protein induction by environmental stimuli are regulated at the transcriptional and posttranscriptional levels. Taken together, the posttranscriptional regulation of RNA transport mediated by EgRBP42 may change the stress-responsive protein profiles under abiotic stress conditions leading to a better adaptation of plants to environmental changes.
Collapse
Affiliation(s)
- Wan-Chin Yeap
- Sime Darby Plantation Berhad, Research and Development, Biotechnology and Breeding, Sime Darby Technology Centre Sdn. Bhd., Serdang, Malaysia
| | - Parameswari Namasivayam
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Tony Eng Keong Ooi
- Sime Darby Plantation Berhad, Research and Development, Biotechnology and Breeding, Sime Darby Technology Centre Sdn. Bhd., Serdang, Malaysia
| | - David Ross Appleton
- Sime Darby Plantation Berhad, Research and Development, Biotechnology and Breeding, Sime Darby Technology Centre Sdn. Bhd., Serdang, Malaysia
| | - Harikrishna Kulaveerasingam
- Sime Darby Plantation Berhad, Research and Development, Sime Darby Research Sdn Bhd, R&D Centre-Upstream, Kuala Langat, Malaysia
| | - Chai-Ling Ho
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- Institute of Plantation Studies, Universiti Putra Malaysia, Serdang, Malaysia
| |
Collapse
|
11
|
Lenka SK, Singh AK, Muthusamy SK, Smita S, Chinnusamy V, Bansal KC. Heterologous expression of rice RNA-binding glycine-rich (RBG) gene OsRBGD3 in transgenic Arabidopsis thaliana confers cold stress tolerance. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:482-491. [PMID: 30940336 DOI: 10.1071/fp18241] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
Imparting cold stress tolerance to crops is a major challenge in subtropical agriculture. New genes conferring cold tolerance needs to be identified and characterised for sustainable crop production in low-temperature stress affected areas. Here we report functional characterisation of OsRBGD3, classified previously as a class D glycine-rich RNA recognition motif (RRM) containing proteins from a drought-tolerant Indica rice cultivar N22. The gene was isolated by screening yeast one-hybrid library using the minimal promoter region of the OsMYB38 that is necessary for cold stress-responsive expression. OsRBGD3 exhibited cold, drought and salt stress inductive expression in a drought tolerant N22 rice cultivar as compared with susceptible variety IR64. OsRBGD3 was found to be localised to both nuclear and cytoplasmic subcellular destinations. Constitutive overexpression of the OsRBGD3 in transgenic Arabidopsis conferred tolerance to cold stress. ABA sensitivity was also observed in transgenic lines suggesting the regulatory role of this gene in the ABA signalling pathway. OsRBGD3 overexpression also attributed to significant root development and early flowering in transgenics. Hence, OsRBGD3 could be an important target for developing cold tolerant early flowering rice and other crops' genotypes for increasing production in low temperature affected areas.
Collapse
Affiliation(s)
- Sangram K Lenka
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, 110003, India
| | - Amit K Singh
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Senthilkumar K Muthusamy
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, 695017, India
| | - Shuchi Smita
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and Department of Immunology, School of Medicine, University of Pittsburgh, PA 15261, USA
| | - Viswanathan Chinnusamy
- ICAR-Indian Agricultural Research Institute, Division of Plant Physiology, New Delhi, 110012, India
| | - Kailash C Bansal
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, 110003, India; and Corresponding author.
| |
Collapse
|
12
|
Nakaminami K, Seki M. RNA Regulation in Plant Cold Stress Response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1081:23-44. [PMID: 30288702 DOI: 10.1007/978-981-13-1244-1_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In addition to plants, all organisms react to environmental stimuli via the perception of signals and subsequently respond through alterations of gene expression. However, genes/mRNAs are usually not the functional unit themselves, and instead, resultant protein products with individual functions result in various acquired phenotypes. In order to fully characterize the adaptive responses of plants to environmental stimuli, it is essential to determine the level of proteins, in addition to the regulation of mRNA expression. This regulatory step, which is referred to as "mRNA posttranscriptional regulation," occurs subsequent to mRNA transcription and prior to translation. Although these RNA regulatory mechanisms have been well-studied in many organisms, including plants, it is not fully understood how plants respond to environmental stimuli, such as cold stress, via these RNA regulations.A recent study described several RNA regulatory factors in relation to environmental stress responses, including plant cold stress tolerance. In this chapter, the functions of RNA regulatory factors and comprehensive analyses related to the RNA regulations involved in cold stress response are summarized, such as mRNA maturation, including capping, splicing, polyadenylation of mRNA, and the quality control system of mRNA; mRNA degradation, including the decapping step; and mRNA stabilization. In addition, the putative roles of messenger ribonucleoprotein (mRNP) granules, such as processing bodies (PBs) and stress granules (SGs), which are cytoplasmic particles, are described in relation to RNA regulations under stress conditions. These RNA regulatory systems are important for adjusting or fine-tuning and determining the final levels of mRNAs and proteins in order to adapt or respond to environmental stresses. Collectively, these new areas of study revealed that plants possess precise novel regulatory mechanisms which specifically function in the response to cold stress.
Collapse
Affiliation(s)
- Kentaro Nakaminami
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- Plant Epigenome Regulation Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Saitama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST), Kawaguchi, Saitama, Japan
| |
Collapse
|
13
|
Czolpinska M, Rurek M. Plant Glycine-Rich Proteins in Stress Response: An Emerging, Still Prospective Story. FRONTIERS IN PLANT SCIENCE 2018; 9:302. [PMID: 29568308 PMCID: PMC5852109 DOI: 10.3389/fpls.2018.00302] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/21/2018] [Indexed: 05/21/2023]
Abstract
Seed plants are sessile organisms that have developed a plethora of strategies for sensing, avoiding, and responding to stress. Several proteins, including the glycine-rich protein (GRP) superfamily, are involved in cellular stress responses and signaling. GRPs are characterized by high glycine content and the presence of conserved segments including glycine-containing structural motifs composed of repetitive amino acid residues. The general structure of this superfamily facilitates division of GRPs into five main subclasses. Although the participation of GRPs in plant stress response has been indicated in numerous model and non-model plant species, relatively little is known about the key physiological processes and molecular mechanisms in which those proteins are engaged. Class I, II, and IV members are known to be involved in hormone signaling, stress acclimation, and floral development, and are crucial for regulation of plant cells growth. GRPs of class IV [RNA-binding proteins (RBPs)] are involved in alternative splicing or regulation of transcription and stomatal movement, seed, pollen, and stamen development; their accumulation is regulated by the circadian clock. Owing to the fact that the overexpression of GRPs can confer tolerance to stress (e.g., some are involved in cold acclimation and may improve growth at low temperatures), these proteins could play a promising role in agriculture through plant genetic engineering. Consequently, isolation, cloning, characterization, and functional validation of novel GRPs expressed in response to the diverse stress conditions are expected to be growing areas of research in the coming years. According to our knowledge, this is the first comprehensive review on participation of plant GRPs in the response to diverse stress stimuli.
Collapse
|
14
|
Covarrubias AA, Cuevas-Velazquez CL, Romero-Pérez PS, Rendón-Luna DF, Chater CCC. Structural disorder in plant proteins: where plasticity meets sessility. Cell Mol Life Sci 2017; 74:3119-3147. [PMID: 28643166 PMCID: PMC11107788 DOI: 10.1007/s00018-017-2557-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 01/08/2023]
Abstract
Plants are sessile organisms. This intriguing nature provokes the question of how they survive despite the continual perturbations caused by their constantly changing environment. The large amount of knowledge accumulated to date demonstrates the fascinating dynamic and plastic mechanisms, which underpin the diverse strategies selected in plants in response to the fluctuating environment. This phenotypic plasticity requires an efficient integration of external cues to their growth and developmental programs that can only be achieved through the dynamic and interactive coordination of various signaling networks. Given the versatility of intrinsic structural disorder within proteins, this feature appears as one of the leading characters of such complex functional circuits, critical for plant adaptation and survival in their wild habitats. In this review, we present information of those intrinsically disordered proteins (IDPs) from plants for which their high level of predicted structural disorder has been correlated with a particular function, or where there is experimental evidence linking this structural feature with its protein function. Using examples of plant IDPs involved in the control of cell cycle, metabolism, hormonal signaling and regulation of gene expression, development and responses to stress, we demonstrate the critical importance of IDPs throughout the life of the plant.
Collapse
Affiliation(s)
- Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico.
| | - Cesar L Cuevas-Velazquez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
| | - Paulette S Romero-Pérez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
| | - David F Rendón-Luna
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
| | - Caspar C C Chater
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
| |
Collapse
|
15
|
Shi X, Hanson MR, Bentolila S. Functional diversity of Arabidopsis organelle-localized RNA-recognition motif-containing proteins. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28371504 DOI: 10.1002/wrna.1420] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/23/2017] [Accepted: 02/24/2017] [Indexed: 12/20/2022]
Abstract
RNA-Binding Proteins (RBPs) play key roles in plant gene expression and regulation. RBPs contain a variety of RNA-binding motifs, the most abundant and most widespread one in eukaryotes is the RNA recognition motif (RRM). Many nucleus-encoded RRM-containing proteins are transported into chloroplasts and/or mitochondria, and participate in various RNA-related processes in plant organelles. Loss of these proteins can have a detrimental effect on some critical processes such as photosynthesis and respiration, sometimes leading to lethality. Progress has been made in the last few years in understanding the function of particular organelle-localized RRM-containing proteins. Members of the Organelle RRM protein (ORRM, some also characterized as Glycine-Rich RNA-Binding Proteins) family and the Chloroplast RiboNucleoProtein (cpRNP) family, are involved in various types of RNA metabolism, including RNA editing, RNA stability and RNA processing. Organelle-localized RRM proteins also function in plant development and stress responses, in some conditions acting as protein or RNA chaperones. There has been recent progress in characterizing the function of organelle-localized RRM proteins in RNA-related processes and how RRM proteins contribute to the normal growth and development of plants. WIREs RNA 2017, 8:e1420. doi: 10.1002/wrna.1420 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Xiaowen Shi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Stephane Bentolila
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| |
Collapse
|
16
|
Wang L, Xie X, Yao W, Wang J, Ma F, Wang C, Yang Y, Tong W, Zhang J, Xu Y, Wang X, Zhang C, Wang Y. RING-H2-type E3 gene VpRH2 from Vitis pseudoreticulata improves resistance to powdery mildew by interacting with VpGRP2A. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1669-1687. [PMID: 28369599 DOI: 10.1093/jxb/erx033] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Grapevine is one of the world's most important fruit crops. European cultivated grape species have the best fruit quality but show almost no resistance to powdery mildew (PM). PM caused by Uncinula necator is a harmful disease that has a significant impact on the economic value of the grape crop. In this study, we examined a RING-H2-type ubiquitin ligase gene VpRH2 that is associated with significant PM-resistance of Chinese wild-growing grape Vitis pseudoreticulata accession Baihe-35-1. The expression of VpRH2 was clearly induced by U. necator inoculation compared with its homologous gene VvRH2 in a PM-susceptible grapevine V. vinifera cv. Thompson Seedless. Using a yeast two-hybrid assay we confirmed that VpRH2 interacted with VpGRP2A, a glycine-rich RNA-binding protein. The degradation of VpGRP2A was inhibited by treatment with the proteasome inhibitor MG132 while VpRH2 did not promote the degradation of VpGRP2A. Instead, the transcripts of VpRH2 were increased by over-expressing VpGRP2A while VpRH2 suppressed the expression of VpGRP2A. Furthermore, VpGRP2A was down-regulated in both Baihe-35-1 and Thompson Seedless after U. necator inoculation. Specifically, we generated VpRH2 overexpression transgenic lines in Thompson Seedless and found that the transgenic plants showed enhanced resistance to powdery mildew compared with the wild-type. In summary, our results indicate that VpRH2 interacts with VpGRP2A and plays a positive role in resistance to powdery mildew.
Collapse
Affiliation(s)
- Lei Wang
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, the People's Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
| | - Xiaoqing Xie
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, the People's Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
| | - Wenkong Yao
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, the People's Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
| | - Jie Wang
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, the People's Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
| | - Fuli Ma
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, the People's Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
| | - Chen Wang
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, the People's Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
| | - Yazhou Yang
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, the People's Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
| | - Weihuo Tong
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, the People's Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
| | - Jianxia Zhang
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, the People's Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
| | - Yan Xu
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, the People's Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
| | - Xiping Wang
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, the People's Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
| | - Chaohong Zhang
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, the People's Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
| | - Yuejin Wang
- College of Horticulture, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, the People's Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, Shaanxi, 712100, the People's Republic of China
| |
Collapse
|
17
|
Ectopic Expression of Plant RNA Chaperone Offering Multiple Stress Tolerance in E. coli. Mol Biotechnol 2017; 59:66-72. [DOI: 10.1007/s12033-017-9992-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
18
|
Wu Z, Zhu D, Lin X, Miao J, Gu L, Deng X, Yang Q, Sun K, Zhu D, Cao X, Tsuge T, Dean C, Aoyama T, Gu H, Qu LJ. RNA Binding Proteins RZ-1B and RZ-1C Play Critical Roles in Regulating Pre-mRNA Splicing and Gene Expression during Development in Arabidopsis. THE PLANT CELL 2016; 28:55-73. [PMID: 26721863 PMCID: PMC4746689 DOI: 10.1105/tpc.15.00949] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/18/2015] [Accepted: 12/28/2015] [Indexed: 05/19/2023]
Abstract
Nuclear-localized RNA binding proteins are involved in various aspects of RNA metabolism, which in turn modulates gene expression. However, the functions of nuclear-localized RNA binding proteins in plants are poorly understood. Here, we report the functions of two proteins containing RNA recognition motifs, RZ-1B and RZ-1C, in Arabidopsis thaliana. RZ-1B and RZ-1C were localized to nuclear speckles and interacted with a spectrum of serine/arginine-rich (SR) proteins through their C termini. RZ-1C preferentially bound to purine-rich RNA sequences in vitro through its N-terminal RNA recognition motif. Disrupting the RNA binding activity of RZ-1C with SR proteins through overexpression of the C terminus of RZ-1C conferred defective phenotypes similar to those observed in rz-1b rz-1c double mutants, including delayed seed germination, reduced stature, and serrated leaves. Loss of function of RZ-1B and RZ-1C was accompanied by defective splicing of many genes and global perturbation of gene expression. In addition, we found that RZ-1C directly targeted FLOWERING LOCUS C (FLC), promoting efficient splicing of FLC introns and likely also repressing FLC transcription. Our findings highlight the critical role of RZ-1B/1C in regulating RNA splicing, gene expression, and many key aspects of plant development via interaction with proteins including SR proteins.
Collapse
Affiliation(s)
- Zhe Wu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611-0011, Japan
| | - Danling Zhu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaoya Lin
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Jin Miao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Lianfeng Gu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fujian 350002, China
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Yang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Kangtai Sun
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tomohiko Tsuge
- Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611-0011, Japan
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Takashi Aoyama
- Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611-0011, Japan
| | - Hongya Gu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China National Plant Gene Research Center, Beijing 100101, China
| | - Li-Jia Qu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China National Plant Gene Research Center, Beijing 100101, China
| |
Collapse
|
19
|
Lewinski M, Hallmann A, Staiger D. Genome-wide identification and phylogenetic analysis of plant RNA binding proteins comprising both RNA recognition motifs and contiguous glycine residues. Mol Genet Genomics 2015; 291:763-73. [DOI: 10.1007/s00438-015-1144-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/06/2015] [Indexed: 11/28/2022]
|
20
|
Chen Y, Zong J, Tan Z, Li L, Hu B, Chen C, Chen J, Liu J. Systematic mining of salt-tolerant genes in halophyte-Zoysia matrella through cDNA expression library screening. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 89:44-52. [PMID: 25689412 DOI: 10.1016/j.plaphy.2015.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 02/10/2015] [Indexed: 06/04/2023]
Abstract
Though a large number of salt-tolerant genes were identified from Glycophyte in previous study, genes involved in salt-tolerance of halophyte were scarcely studied. In this report, an important halophyte turfgrass, Zoysia matrella, was used for systematic excavation of salt-tolerant genes using full-length cDNA expression library in yeast. Adopting the Gateway-compatible vector system, a high quality entry library was constructed, containing 3 × 10(6) clones with an average inserted fragments length of 1.64 kb representing a 100% full-length rate. The yeast expression library was screened in a salt-sensitive yeast mutant. The screening yielded dozens of salt-tolerant clones harboring 16 candidate salt-tolerant genes. Under salt-stress condition, these 16 genes exhibited different transcription levels. According to the results, we concluded that the salt-tolerance of Z. matrella might result from known genes involved in ion regulation, osmotic adjustment, as well as unknown pathway associated with protein folding and modification, RNA metabolism, and mitochondrial membrane translocase, etc. In addition, these results shall provide new insight for the future researches with respect to salt-tolerance.
Collapse
Affiliation(s)
- Yu Chen
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Institute of Botany, Jiangsu Province & Chinese Academy of Sciences, Nanjing 210014, China; College of Ago-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Junqin Zong
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Institute of Botany, Jiangsu Province & Chinese Academy of Sciences, Nanjing 210014, China
| | - Zhiqun Tan
- College of Ago-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Lanlan Li
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Institute of Botany, Jiangsu Province & Chinese Academy of Sciences, Nanjing 210014, China
| | - Baoyun Hu
- College of Ago-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuanming Chen
- College of Ago-grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingbo Chen
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Institute of Botany, Jiangsu Province & Chinese Academy of Sciences, Nanjing 210014, China
| | - Jianxiu Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Institute of Botany, Jiangsu Province & Chinese Academy of Sciences, Nanjing 210014, China.
| |
Collapse
|
21
|
Dobrá J, Černý M, Štorchová H, Dobrev P, Skalák J, Jedelský PL, Lukšanová H, Gaudinová A, Pešek B, Malbeck J, Vanek T, Brzobohatý B, Vanková R. The impact of heat stress targeting on the hormonal and transcriptomic response in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 231:52-61. [PMID: 25575991 DOI: 10.1016/j.plantsci.2014.11.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/29/2014] [Accepted: 11/18/2014] [Indexed: 05/18/2023]
Abstract
Targeting of the heat stress (HS, 40°C) to shoots, roots or whole plants substantially affects Arabidopsis physiological responses. Effective stress targeting was proved by determination of the expression of HS markers, HsfA2 and HSA32, which were quickly stimulated in the targeted organ(s), but remained low in non-stressed tissues for at least 2h. When shoots or whole plants were subjected to HS, a transient decrease in abscisic acid, accompanied by a small increase in active cytokinin levels, was observed in leaves, consistent with stimulation of transpiration, the main cooling mechanism in leaves. HS application targeted to part of plant resulted in a rapid stimulation of expression of components of cytokinin signaling pathway (especially of receptor genes) in the non-exposed tissues, which indicated fast inter-organ communication. Under all HS treatments, shoot apices responded by transient elevation of active cytokinin contents and stimulation of transcription of genes involved in photosynthesis and carbohydrate metabolism. Duration of this stimulation was negatively correlated with stress strength. The impact of targeted HS on the expression of 63 selected genes, including those coding regulatory 14-3-3 proteins, was compared. Stimulation of GRF9 (GRF14μ) in stressed organs after 2-6h may be associated with plant stress adaptation.
Collapse
Affiliation(s)
- Jana Dobrá
- Institute of Experimental Botany AS CR, Rozvojová 263, CZ-16502 Prague 6, Czech Republic.
| | - Martin Černý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC-Central European Institute of Technology, Mendel University in Brno, CZ-61300 Brno, Czech Republic.
| | - Helena Štorchová
- Institute of Experimental Botany AS CR, Rozvojová 263, CZ-16502 Prague 6, Czech Republic.
| | - Petre Dobrev
- Institute of Experimental Botany AS CR, Rozvojová 263, CZ-16502 Prague 6, Czech Republic.
| | - Jan Skalák
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC-Central European Institute of Technology, Mendel University in Brno, CZ-61300 Brno, Czech Republic.
| | - Petr L Jedelský
- Faculty of Science, Charles University, Viničná 7, CZ-12843 Prague, Czech Republic.
| | - Hana Lukšanová
- Institute of Experimental Botany AS CR, Rozvojová 263, CZ-16502 Prague 6, Czech Republic.
| | - Alena Gaudinová
- Institute of Experimental Botany AS CR, Rozvojová 263, CZ-16502 Prague 6, Czech Republic.
| | - Bedřich Pešek
- Institute of Experimental Botany AS CR, Rozvojová 263, CZ-16502 Prague 6, Czech Republic.
| | - Jiří Malbeck
- Institute of Experimental Botany AS CR, Rozvojová 263, CZ-16502 Prague 6, Czech Republic.
| | - Tomas Vanek
- Institute of Experimental Botany AS CR, Rozvojová 263, CZ-16502 Prague 6, Czech Republic.
| | - Břetislav Brzobohatý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC-Central European Institute of Technology, Mendel University in Brno, CZ-61300 Brno, Czech Republic.
| | - Radomíra Vanková
- Institute of Experimental Botany AS CR, Rozvojová 263, CZ-16502 Prague 6, Czech Republic.
| |
Collapse
|
22
|
Hodgins KA, Bock DG, Hahn MA, Heredia SM, Turner KG, Rieseberg LH. Comparative genomics in the Asteraceae reveals little evidence for parallel evolutionary change in invasive taxa. Mol Ecol 2015; 24:2226-40. [PMID: 25439241 DOI: 10.1111/mec.13026] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/23/2014] [Accepted: 11/26/2014] [Indexed: 01/12/2023]
Abstract
Asteraceae, the largest family of flowering plants, has given rise to many notorious invasive species. Using publicly available transcriptome assemblies from 35 Asteraceae, including six major invasive species, we examined evidence for micro- and macro-evolutionary genomic changes associated with invasion. To detect episodes of positive selection repeated across multiple introductions, we conducted comparisons between native and introduced genotypes from six focal species and identified genes with elevated rates of amino acid change (dN/dS). We then looked for evidence of positive selection at a broader phylogenetic scale across all taxa. As invasive species may experience founder events during colonization and spread, we also looked for evidence of increased genetic load in introduced genotypes. We rarely found evidence for parallel changes in orthologous genes in the intraspecific comparisons, but in some cases we identified changes in members of the same gene family. Using among-species comparisons, we detected positive selection in 0.003-0.69% and 2.4-7.8% of the genes using site and stochastic branch-site models, respectively. These genes had diverse putative functions, including defence response, stress response and herbicide resistance, although there was no clear pattern in the GO terms. There was no indication that introduced genotypes have a higher proportion of deleterious alleles than native genotypes in the six focal species, suggesting multiple introductions and admixture mitigated the impact of drift. Our findings provide little evidence for common genomic responses in invasive taxa of the Asteraceae and hence suggest that multiple evolutionary pathways may lead to adaptation during introduction and spread in these species.
Collapse
Affiliation(s)
- Kathryn A Hodgins
- School of Biological Sciences, Monash University, Clayton, Vic., 3800, Australia
| | | | | | | | | | | |
Collapse
|
23
|
Abstract
Bacterial cold shock proteins (CSPs) function as RNA chaperones that destabilize RNA secondary structures. A quadruple mutant of Escherichia coli (cspA, cspB, cspG, and cspE) displays a cold-sensitive growth phenotype. Plant cold shock domain (CSD) proteins have been shown to complement the cold-sensitive phenotype of the E. coli mutant and to share a function with E. coli CSPs as RNA chaperones. This methodology, which is detailed here, can be utilized to reveal or probe the RNA chaperone activity of heterologous proteins.
Collapse
Affiliation(s)
- Myung-Hee Kim
- Crop Breeding Research Division, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Hitsujigaoka, Sapporo, 062-8555, Japan
| | | |
Collapse
|
24
|
Tripet B, Mason KE, Eilers BJ, Burns J, Powell P, Fischer AM, Copié V. Structural and biochemical analysis of the Hordeum vulgare L. HvGR-RBP1 protein, a glycine-rich RNA-binding protein involved in the regulation of barley plant development and stress response. Biochemistry 2014; 53:7945-60. [PMID: 25495582 PMCID: PMC4278681 DOI: 10.1021/bi5007223] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 11/25/2014] [Indexed: 12/26/2022]
Abstract
The timing of whole-plant senescence influences important agricultural traits such as yield and grain protein content. Post-transcriptional regulation by plant RNA-binding proteins is essential for proper control of gene expression, development, and stress responses. Here, we report the three-dimensional solution NMR structure and nucleic acid-binding properties of the barley glycine-rich RNA-binding protein HvGR-RBP1, whose transcript has been identified as being >45-fold up-regulated in early-as compared to late-senescing near-isogenic barley germplasm. NMR analysis reveals that HvGR-RBP1 is a multidomain protein comprising a well-folded N-terminal RNA Recognition Motif (RRM) and a structurally disordered C-terminal glycine-rich domain. Chemical shift differences observed in 2D (1)H-(15)N correlation (HSQC) NMR spectra of full-length HvGR-RBP1 and N-HvGR-RBP1 (RRM domain only) suggest that the two domains can interact both in-trans and intramolecularly, similar to what is observed in the tobacco NtGR-RBP1 protein. Further, we show that the RRM domain of HvGR-RBP1 binds single-stranded DNA nucleotide fragments containing the consensus nucleotide sequence 5'-TTCTGX-3' with low micromolar affinity in vitro. We also demonstrate that the C-terminal glycine-rich (HvGR) domain of Hv-GR-RBP1 can interact nonspecifically with ssRNA in vitro. Structural similarities with other plant glycine-rich RNA-binding proteins suggest that HvGR-RBP1 may be multifunctional. Based on gene expression analysis following cold stress in barley and E. coli growth studies following cold shock treatment, we conclude that HvGR-RBP1 functions in a manner similar to cold-shock proteins and harbors RNA chaperone activity. HvGR-RBP1 is therefore not only involved in the regulation of barley development including senescence, but also functions in plant responses to environmental stress.
Collapse
MESH Headings
- Cold-Shock Response/physiology
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Plant/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Hordeum/genetics
- Hordeum/metabolism
- Plant Proteins/chemistry
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Protein Binding
- Protein Structure, Tertiary
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
Collapse
Affiliation(s)
- Brian
P. Tripet
- Department of Chemistry and Biochemistry and Department of Plant
Sciences and Plant
Pathology, Montana State University, Bozeman, Montana 59717, United States
| | - Katelyn E. Mason
- Department of Chemistry and Biochemistry and Department of Plant
Sciences and Plant
Pathology, Montana State University, Bozeman, Montana 59717, United States
| | - Brian J. Eilers
- Department of Chemistry and Biochemistry and Department of Plant
Sciences and Plant
Pathology, Montana State University, Bozeman, Montana 59717, United States
| | - Jennifer Burns
- Department of Chemistry and Biochemistry and Department of Plant
Sciences and Plant
Pathology, Montana State University, Bozeman, Montana 59717, United States
| | - Paul Powell
- Department of Chemistry and Biochemistry and Department of Plant
Sciences and Plant
Pathology, Montana State University, Bozeman, Montana 59717, United States
| | - Andreas M. Fischer
- Department of Chemistry and Biochemistry and Department of Plant
Sciences and Plant
Pathology, Montana State University, Bozeman, Montana 59717, United States
| | - Valérie Copié
- Department of Chemistry and Biochemistry and Department of Plant
Sciences and Plant
Pathology, Montana State University, Bozeman, Montana 59717, United States
| |
Collapse
|
25
|
Yeap WC, Namasivayam P, Ho CL. HnRNP-like proteins as post-transcriptional regulators. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 227:90-100. [PMID: 25219311 DOI: 10.1016/j.plantsci.2014.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 07/17/2014] [Accepted: 07/18/2014] [Indexed: 05/23/2023]
Abstract
Plant cells contain a diverse repertoire of RNA-binding proteins (RBPs) that coordinate a network of post-transcriptional regulation. RBPs govern diverse developmental processes by modulating the gene expression of specific transcripts. Recent gene annotation and RNA sequencing clearly showed that heterogeneous nuclear ribonucleoprotein (hnRNP)-like proteins which form a family of RBPs, are also expressed in higher plants and serve specific plant functions. In addition to their involvement in post-transcriptional regulation from mRNA capping to translation, they are also involved in telomere regulation, gene silencing and regulation in chloroplast. Here, we review the involvement of plant hnRNP-like proteins in post-transcription regulation of RNA processes and their functional roles in control of plant developmental processes especially plant-specific functions including flowering, chloroplastic-specific mRNA regulation, long-distance phloem transportation and plant responses to environmental stresses.
Collapse
Affiliation(s)
- Wan-Chin Yeap
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Sime Darby Technology Centre Sdn. Bhd., 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Parameswari Namasivayam
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Chai-Ling Ho
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| |
Collapse
|
26
|
Khan F, Daniëls MA, Folkers GE, Boelens R, Saqlan Naqvi SM, van Ingen H. Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: implications for its RNA chaperone function. Nucleic Acids Res 2014; 42:8705-18. [PMID: 24957607 PMCID: PMC4117745 DOI: 10.1093/nar/gku468] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 04/30/2014] [Accepted: 05/12/2014] [Indexed: 12/30/2022] Open
Abstract
Glycine-rich RNA-binding proteins (GR-RBPs) are involved in cold shock response of plants as RNA chaperones facilitating mRNA transport, splicing and translation. GR-RBPs are bipartite proteins containing a RNA recognition motif (RRM) followed by a glycine-rich region. Here, we studied the structural basis of nucleic acid binding of full-length Nicotiana tabacum GR-RBP1. NMR studies of NtGR-RBP1 show that the glycine-rich domain, while intrinsically disordered, is responsible for mediating self-association by transient interactions with its RRM domain (NtRRM). Both NtGR-RBP1 and NtRRM bind specifically and with low micromolar affinity to RNA and single-stranded DNA. The solution structure of NtRRM shows that it is a canonical RRM domain. A HADDOCK model of the NtRRM-RNA complex, based on NMR chemical shift and NOE data, shows that nucleic acid binding results from a combination of stacking and electrostatic interactions with conserved RRM residues. Finally, DNA melting experiments demonstrate that NtGR-RBP1 is more efficient in melting CTG containing nucleic acids than isolated NtRRM. Together, our study supports the model that self-association of GR-RBPs by the glycine-rich region results in cooperative unfolding of non-native substrate structures, thereby enhancing its chaperone function.
Collapse
Affiliation(s)
- Fariha Khan
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands Department of Biochemistry, PMAS Agriculture University Rawalpindi, 46300 Rawalpindi, Pakistan
| | - Mark A Daniëls
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Gert E Folkers
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Rolf Boelens
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - S M Saqlan Naqvi
- Department of Biochemistry, PMAS Agriculture University Rawalpindi, 46300 Rawalpindi, Pakistan
| | - Hugo van Ingen
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
27
|
Lee K, Lee HJ, Kim DH, Jeon Y, Pai HS, Kang H. A nuclear-encoded chloroplast protein harboring a single CRM domain plays an important role in the Arabidopsis growth and stress response. BMC PLANT BIOLOGY 2014; 14:98. [PMID: 24739417 PMCID: PMC4021458 DOI: 10.1186/1471-2229-14-98] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 04/11/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND Although several chloroplast RNA splicing and ribosome maturation (CRM) domain-containing proteins have been characterized for intron splicing and rRNA processing during chloroplast gene expression, the functional role of a majority of CRM domain proteins in plant growth and development as well as chloroplast RNA metabolism remains largely unknown. Here, we characterized the developmental and stress response roles of a nuclear-encoded chloroplast protein harboring a single CRM domain (At4g39040), designated CFM4, in Arabidopsis thaliana. RESULTS Analysis of CFM4-GFP fusion proteins revealed that CFM4 is localized to chloroplasts. The loss-of-function T-DNA insertion mutants for CFM4 (cfm4) displayed retarded growth and delayed senescence, suggesting that CFM4 plays a role in growth and development of plants under normal growth conditions. In addition, cfm4 mutants showed retarded seed germination and seedling growth under stress conditions. No alteration in the splicing patterns of intron-containing chloroplast genes was observed in the mutant plants, but the processing of 16S and 4.5S rRNAs was abnormal in the mutant plants. Importantly, CFM4 was determined to possess RNA chaperone activity. CONCLUSIONS These results suggest that the chloroplast-targeted CFM4, one of two Arabidopsis genes encoding a single CRM domain-containing protein, harbors RNA chaperone activity and plays a role in the Arabidopsis growth and stress response by affecting rRNA processing in chloroplasts.
Collapse
Affiliation(s)
- Kwanuk Lee
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, Korea
| | - Hwa Jung Lee
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, Korea
| | - Dong Hyun Kim
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, Korea
| | - Young Jeon
- Department of Systems Biology, Yonsei University, Seoul 120-749, Korea
| | - Hyun-Sook Pai
- Department of Systems Biology, Yonsei University, Seoul 120-749, Korea
| | - Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, Korea
| |
Collapse
|
28
|
M Ller GL, Triassi A, Alvarez CE, Falcone Ferreyra MAL, Andreo CS, Lara MAV, Drincovich MAF. Circadian oscillation and development-dependent expression of glycine-rich RNA binding proteins in tomato fruits. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:411-423. [PMID: 32481001 DOI: 10.1071/fp13239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 10/22/2013] [Indexed: 06/11/2023]
Abstract
Glycine-rich RNA-binding proteins (GRPs) are involved in the modulation of the post-transcriptional processing of transcripts and participate as an output signal of the circadian clock. However, neither GRPs nor the circadian rhythmic have been studied in detail in fleshy fruits as yet. In the present work, the GRP1 gene family was analysed in Micro-Tom tomato (Solanum lycopersicum L.) fruit. Three highly homologous LeGRP1 genes (LeGRP1a-c) were identified. For each gene, three products were found, corresponding to the unspliced precursor mRNA (pre-mRNA), the mature mRNA and the alternatively spliced mRNA (preLeGRP1a-c, mLeGRP1a-c and asLeGRP1a-c, respectively). Tomato GRPs (LeGRPs) show the classic RNA recognition motif and glycine-rich region, and were found in the nucleus and in the cytosol of tomato fruit. By using different Escherichia coli mutants, it was found that LeGRP1s contained in vivo RNA-melting abilities and were able to complement the cold-sensitive phenotype of BX04 cells. Particular circadian profiles of expression, dependent on the fruits' developmental stage, were found for each LeGRP1 form. During ripening off the vine of fruits harvested at the mature green stage, the levels of all LeGRP1a-c forms drastically increased; however, incubation at 4°C prevented such increases. Analysis of the expression of all LeGRP1a-c forms suggests a positive regulation of expression in tomato fruit. Overall, the results obtained in this work reveal a complex pattern of expression of GRPs in tomato fruit, suggesting they might be involved in post-transcriptional modulation of circadian processes of this fleshy fruit.
Collapse
Affiliation(s)
- Gabriela L M Ller
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Suipacha 531, Rosario (2000), Argentina. Corresponding author.
| | - Agustina Triassi
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Suipacha 531, Rosario (2000), Argentina
| | - Clarisa E Alvarez
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Suipacha 531, Rosario (2000), Argentina
| | - Mar A L Falcone Ferreyra
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Suipacha 531, Rosario (2000), Argentina
| | - Carlos S Andreo
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Suipacha 531, Rosario (2000), Argentina
| | - Mar A V Lara
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Suipacha 531, Rosario (2000), Argentina
| | - Mar A F Drincovich
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Suipacha 531, Rosario (2000), Argentina
| |
Collapse
|
29
|
Cold acclimation induces freezing tolerance via antioxidative enzymes, proline metabolism and gene expression changes in two chrysanthemum species. Mol Biol Rep 2014; 41:815-22. [DOI: 10.1007/s11033-013-2921-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 12/18/2013] [Indexed: 11/26/2022]
|
30
|
Han JH, Jung YJ, Lee HJ, Jung HS, Lee KO, Kang H. The RNA chaperone and protein chaperone activity of Arabidopsis glycine-rich RNA-binding protein 4 and 7 is determined by the propensity for the formation of high molecular weight complexes. Protein J 2013; 32:449-55. [PMID: 23912241 DOI: 10.1007/s10930-013-9504-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
RNA chaperones and protein chaperones are cellular proteins that can aid the correct folding of target RNAs and proteins, respectively. Although many proteins possessing RNA chaperone or protein chaperone activity have been demonstrated in diverse organisms, report evaluating the RNA chaperone and protein chaperone activity of a given protein is severely limited. Here, two glycine-rich RNA-binding proteins in Arabidopsis thaliana (AtGRPs), AtGRP7 exhibiting RNA chaperone activity and AtGRP4 exhibiting no RNA chaperone activity, were investigated for their protein chaperone activity. The heat-induced thermal aggregation of a substrate protein was significantly decreased with the addition of AtGRP4 depending on protein concentration, whereas the thermal aggregation of a substrate protein was further increased with the addition of AtGRP7, demonstrating that AtGRP4 but not AtGRP7 possesses protein chaperone activity. Size exclusion chromatography and electron microscopy analyses revealed that the formation of high molecular weight (HMW) complexes is closely related to the protein chaperone activity of AtGRP4. Importantly, the additional 25 amino acids at the N-terminus of AtGRP4 are crucial for HMW complex formation and protein chaperone activity. Taken together, these results show that the formation of HMW complexes is important for determining the RNA chaperone and protein chaperone activity of AtGRP4 and AtGRP7.
Collapse
Affiliation(s)
- Ji Hoon Han
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Kwangju, 500-757, Korea
| | | | | | | | | | | |
Collapse
|
31
|
Wang R, Gao F, Guo BQ, Huang JC, Wang L, Zhou YJ. Short-term chromium-stress-induced alterations in the maize leaf proteome. Int J Mol Sci 2013; 14:11125-44. [PMID: 23712354 PMCID: PMC3709723 DOI: 10.3390/ijms140611125] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/25/2013] [Accepted: 05/15/2013] [Indexed: 11/16/2022] Open
Abstract
Soil contamination by chromium (Cr) has become an increasing problem worldwide as a result of extensive industrial activities. Chromium, especially hexavalent Cr, impairs the growth and productivity of plants. Although it has been proposed that plants could modify their metabolism to adapt to Cr stress by reprogramming the expression of genes, especially those related to the antioxidant system, damage response, and electron transport chain, evidence at the protein expression level is lacking. To better understand the precise mechanisms underlying Cr phytoxicity and the plant response to Cr exposure, the time-course of changes in the protein expression profile induced by short-term hexavalent Cr exposure (1, 6 and 24 h) were analyzed in maize leaves. Among the over 1200 protein spots detected reproducibly by two-dimensional electrophoresis (2-DE), 60 were found to be differentially accumulated during Cr stress treatment. Of the Cr-regulated proteins, 58 were identified using tandem mass spectrometry (MS/MS). The Cr-regulated proteins identified were mainly involved in ROS detoxification and defense responses (26%), photosynthesis and chloroplast organization (22%), post-transcriptional processing of mRNA and rRNA (12%), protein synthesis and folding (10%), the DNA damage response (5%), and the cytoskeleton (3%). The possible involvement of these Cr stress-responsive proteins in Cr phytoxicity and the plant response to Cr exposure in maize is discussed, taking into consideration the information available from other plant models. Our results provide preliminary evidence that will facilitate understanding the molecular mechanisms underlying Cr toxicity in maize.
Collapse
Affiliation(s)
- Rong Wang
- College of Life Science, Fuyang Teachers College, Fuyang 236037, China; E-Mails: (R.W.); (J.-C.H.)
| | - Fei Gao
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; E-Mails: (F.G.); (B.-Q.G.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bing-Qian Guo
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; E-Mails: (F.G.); (B.-Q.G.)
| | - Ji-Chang Huang
- College of Life Science, Fuyang Teachers College, Fuyang 236037, China; E-Mails: (R.W.); (J.-C.H.)
| | - Lei Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Authors to whom correspondence should be addressed; E-Mails: (L.W.); (Y.-J.Z.); Tel./Fax: +86-10-8210-6134 (L.W.); +86-10-6893-2922 (Y.-J.Z.)
| | - Yi-Jun Zhou
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; E-Mails: (F.G.); (B.-Q.G.)
- Authors to whom correspondence should be addressed; E-Mails: (L.W.); (Y.-J.Z.); Tel./Fax: +86-10-8210-6134 (L.W.); +86-10-6893-2922 (Y.-J.Z.)
| |
Collapse
|
32
|
Kang H, Park SJ, Kwak KJ. Plant RNA chaperones in stress response. TRENDS IN PLANT SCIENCE 2013; 18:100-6. [PMID: 22947615 DOI: 10.1016/j.tplants.2012.08.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 08/02/2012] [Accepted: 08/13/2012] [Indexed: 05/18/2023]
Abstract
Post-transcriptional regulation of RNA metabolism is a key regulatory process in diverse cellular processes, including the stress response of plants, during which a variety of RNA-binding proteins (RBPs) function as central regulators in cells. RNA chaperones are RBPs found in all living organisms and function by providing assistance to the correct folding of RNA molecules during RNA metabolism. Although our understanding of the role of RNA chaperones in plants is far less advanced than in bacteria, viruses, and animals, recent progress in functional characterization and determination of RNA chaperone activity of several RBPs has shed new light on the emerging roles of RNA chaperones during the stress response of plants.
Collapse
Affiliation(s)
- Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757, Korea.
| | | | | |
Collapse
|
33
|
Yeap WC, Ooi TEK, Namasivayam P, Kulaveerasingam H, Ho CL. EgRBP42 encoding an hnRNP-like RNA-binding protein from Elaeis guineensis Jacq. is responsive to abiotic stresses. PLANT CELL REPORTS 2012; 31:1829-1843. [PMID: 22699852 DOI: 10.1007/s00299-012-1297-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 05/31/2012] [Indexed: 06/01/2023]
Abstract
RNA-binding proteins (RBPs) have been implicated as regulatory proteins involved in the post-transcriptional processes of gene expression in plants under various stress conditions. In this study, we report the cloning and characterization of a gene, designated as EgRBP42, encoding a member of the plant heterogeneous nuclear ribonucleoprotein (hnRNP)-like RBP family from oil palm (Elaeis guineensis Jacq.). EgRBP42 consists of two N-terminal RNA recognition motifs and a glycine-rich domain at the C-terminus. The upstream region of EgRBP42 has multiple light-responsive, stress-responsive regulatory elements and regulatory elements associated with flower development. Real-time RT-PCR analysis of EgRBP42 showed that EgRBP42 was expressed in oil palm tissues tested, including leaf, shoot apical meristem, root, female inflorescence, male inflorescence and mesocarp with the lowest transcript level in the roots. EgRBP42 protein interacted with transcripts associated with transcription, translation and stress responses using pull-down assay and electrophoretic mobility shift assay. The accumulation of EgRBP42 and its interacting transcripts were induced by abiotic stresses, including salinity, drought, submergence, cold and heat stresses in leaf discs. Collectively, the data suggested that EgRBP42 is a RBP, which responds to various abiotic stresses and could be advantageous for oil palm under stress conditions. Key message EgRBP42 may be involved in the post-transcriptional regulation of stress-related genes important for plant stress response and adaptation.
Collapse
Affiliation(s)
- Wan-Chin Yeap
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia,
| | | | | | | | | |
Collapse
|
34
|
Narsai R, Law SR, Carrie C, Xu L, Whelan J. In-depth temporal transcriptome profiling reveals a crucial developmental switch with roles for RNA processing and organelle metabolism that are essential for germination in Arabidopsis. PLANT PHYSIOLOGY 2011; 157:1342-62. [PMID: 21908688 PMCID: PMC3252162 DOI: 10.1104/pp.111.183129] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 09/05/2011] [Indexed: 05/20/2023]
Abstract
Germination represents a rapid transition from dormancy to a high level of metabolic activity. In-depth transcriptomic profiling at 10 time points in Arabidopsis (Arabidopsis thaliana), including fresh seed, ripened seed, during stratification, germination, and postgermination per se, revealed specific temporal expression patterns that to our knowledge have not previously been identified. Over 10,000 transcripts were differentially expressed during cold stratification, with subequal numbers up-regulated as down-regulated, revealing an active period in preparing seeds for germination, where transcription and RNA degradation both play important roles in regulating the molecular sequence of events. A previously unidentified transient expression pattern was observed for a group of genes, whereby a significant rise in expression was observed at the end of stratification and significantly lower expression was observed 6 h later. These genes were further defined as germination specific, as they were most highly expressed at this time in germination, in comparison with all developmental tissues in the AtGenExpress data set. Functional analysis of these genes using genetic inactivation revealed that they displayed a significant enrichment for embryo-defective or -arrested phenotype. This group was enriched in genes encoding mitochondrial and nuclear RNA-processing proteins, including more than 45% of all pentatricopeptide domain-containing proteins expressed during germination. The presence of mitochondrial DNA replication factors and RNA-processing functions in this germination-specific subset represents the earliest events in organelle biogenesis, preceding any changes associated with energy metabolism. Green fluorescent protein analysis also confirmed organellar localization for 65 proteins, largely showing germination-specific expression. These results suggest that mitochondrial biogenesis involves a two-step process to produce energetically active organelles: an initial phase at the end of stratification involving mitochondrial DNA synthesis and RNA processing, and a later phase for building the better-known energetic functions. This also suggests that signals with a mitochondrial origin and retrograde signals may be crucial for successful germination.
Collapse
Affiliation(s)
- Reena Narsai
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia.
| | | | | | | | | |
Collapse
|